rs2031367

Variant names:

• chr6-87097462-A-G
• rs2031367

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.387 in 152,168 control chromosomes in the GnomAD database, including 13,782 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (13782 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58768 AN: 152050 Hom.: 13726 Cov.: 33

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.352

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.387 AC: 58877 AN: 152168 Hom.: 13782 Cov.: 33 AF XY: 0.383 AC XY: 28460 AN XY: 74392

African (AFR) AF: 0.668 AC: 27734 AN: 41508

American (AMR) AF: 0.295 AC: 4509 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 847 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1424 AN: 5180

South Asian (SAS) AF: 0.287 AC: 1384 AN: 4826

European-Finnish (FIN) AF: 0.258 AC: 2736 AN: 10590

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.283 AC: 19214 AN: 67994

Other (OTH) AF: 0.357 AC: 752 AN: 2108

Alfa AF: 0.348 Hom.: 4214

Bravo AF: 0.403

Asia WGS AF: 0.372 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.91
DANN	Benign	0.37
PhyloP100		-0.058

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2031367; hg19: chr6-87807180; COSMIC: COSV63644914;